23  PyNRRD

from pyhere import here
import pandas as pd

import nrrd

23.1 seg.nrrd

23.1.1 Print seg.nrrd file Info

import nrrd

def print_seg_nrrd_info(path):
    """Print segment information from NRRD file.
    """
    # Load the NRRD file
    data, header = nrrd.read(path)

    # Initialize a dictionary to store segment information 
    segments_info = {}

    # Loop through metadata to extract segment information
    for i in range(2):  # Assuming 2 segments
        segment_id = header.get(f'Segment{i}_ID', 'N/A')
        label_value = header.get(f'Segment{i}_LabelValue', 'N/A')
        layer = header.get(f'Segment{i}_Layer', 'N/A')
        name = header.get(f'Segment{i}_Name', 'N/A')
        
        # Store information in dictionary
        segments_info[f'Segment_{i}'] = {
            'ID': segment_id,
            'LabelValue': label_value,
            'Layer': layer,
            'Name': name
        }

    # Display the extracted segment information
    for segment, info in segments_info.items():
        print(f"{segment} Info:")
        print(f"  ID: {info['ID']}")
        print(f"  LabelValue: {info['LabelValue']}")
        print(f"  Layer: {info['Layer']}")
        print(f"  Name: {info['Name']}\n")

print_seg_nrrd_info(here("data/MRI-Brain-Eye/Case1/Segmentation.seg.nrrd"))

Segment_0 Info:
  ID: Segment_1
  LabelValue: 1
  Layer: 0
  Name: Segment_LE

Segment_1 Info:
  ID: Segment_2
  LabelValue: 2
  Layer: 0
  Name: Segment_RE

print_seg_nrrd_info(here("data/MRI-Brain-Eye/Case2/Segmentation_Eye.seg.nrrd"))

Segment_0 Info:
  ID: Segment_1
  LabelValue: 1
  Layer: 0
  Name: Segment_LE

Segment_1 Info:
  ID: Segment_2
  LabelValue: 2
  Layer: 0
  Name: Segment_RE

23.1.2 Get Label value by Name

import nrrd

def get_labelvalue_by_name(maskFilepath, name):
    """
    Retrieves the LabelValue of a segment given its name in a segmentation mask file.
    
    Parameters:
    - name (str): The name of the segment (e.g., "Segment_LE" or "Segment_RE").
    - maskFilepath (str): Path to the segmentation mask file (.seg.nrrd).
    
    Returns:
    - int: The LabelValue associated with the given segment name.
    - None: If the segment name is not found.
    """
    # Load the header of the NRRD file
    _, header = nrrd.read(maskFilepath)
    
    # Loop through the header to find the segment with the specified name
    segment_index = 0
    while True:
        # Construct the segment name key
        segment_name_key = f'Segment{segment_index}_Name'
        
        # Check if this segment key exists in the header
        if segment_name_key not in header:
            # If the key does not exist, we have exhausted all segments
            break
        
        # Check if this segment's name matches the specified name
        if header[segment_name_key] == name:
            # If it matches, retrieve the LabelValue for this segment
            label_value_key = f'Segment{segment_index}_LabelValue'
            return int(header[label_value_key])
        
        # Move to the next segment index
        segment_index += 1
    
    # Return None if the segment name was not found
    print(f"Segment with name '{name}' not found in the file '{maskFilepath}'.")
    return None

get_labelvalue_by_name(here("data/MRI-Brain-Eye/Case1/Segmentation.seg.nrrd"), "Segment_LE")

1

get_labelvalue_by_name(here("data/MRI-Brain-Eye/Case1/Segmentation.seg.nrrd"), "Segment_RE")

2